Posts Tagged ‘fungal genomes’

JGI Fungal Jamboree

March 19th, 2012

The annual JGI Fungal Jamboree will start on Monday 19th at the Marriott Hotel in Walnut Creek. During the workshop, attendees will:

  • provide an update on their JGI program’s development during the last year and future plans,
  • discuss several important questions, including: (1) How to address current bottlenecks for future scale-up (target selection, DNA samples, analysis, publications)? (2) How to reach new groups of users and coordinate with other large genomics initiatives (e.g., 1K Chinese Fungal Genomes)? (3) What products in addition to sequencing JGI should be working on for mycologists? (4) What informatics/analytical needs should be addressed?
  • discuss strategic partnerships.

I will report on our two fungal programs, i.e. the Mycorrhizal Genomics Initiative and the Metatranscriptomics of Forest Soils.

    JGI Fungal Jamboree 2012

    February 15th, 2012

    1000 Fungal Genomes Project

    November 11th, 2011

     

    Our proposal to sequence 1000+ fungal genomes has been funded by the Joint Genome Institute (JGI) of the Department of Energy. Our consortium in collaboration with JGI has embarked on a five-year project to sequence 1000 fungal genomes from across the Fungal Tree of Life. The guiding principle for sampling in F1000 is at the end of the project to have 2 representatives from all fungal families or family-level clades. This will require a lot of coordination across several JGI CSP projects, e.g. our Mycorrhizal Genome Initiative, the Forest Soil Metatranscriptome Project and the Saprotrophic Agaricomycotina project, and interactions with the community and systematics experts of given groups.

    The team comprises Joseph Spatafora (Oregon State University), Jason Stajich (University of California at Riverside), Kevin McCluskey (Fungal Genetics Stock Center), Pedro Crous (Centraal Bureau voor Schimmelcultures, Netherlands), Gillian Turgeon (Cornell University), Daniel Lindner (USDA Forest Service), Kerry O’Donnell and Todd Ward (USDA ARS), Antonis Rokas (Vanderbilt University), Louise Glass (University of California at Berkeley), Betsy Arnold (University of Arizona), Igor Grigoriev (JGI DOE) and myself.

    The ‘1000 Fungal Genomes‘ site, set up by Jason Stajich’s group, represents a gathering of the information about the project and will link to additional resources tracking the progress of the project.

    Genomes of Skin Invaders

    February 27th, 2011

    hyphaecolonizinghairPathogenic fungi colonizing human skin, so-called dermatophytes, are a pleague for millions of humans. There are highly specialized filamentous fungi exclusively infecting keratinized animal structures causing mycoses.  Studies of dermatophyte pathogenic interactions have been hampered by a lack of full genome sequences. To provide broad insights into the molecular basis of the pathogenicity-associated traits, Burmester et al. published in the last issue of Genome Biology (2011/12/1/R7)  the first genome sequences of two closely phylogenetically related dermatophytes, Arthroderma benhamiae and Trichophyton verrucosum, both of which induce highly inflammatory infections in humans.

    The genomes of A. benhamiae and T. verrucosum were sequenced by a whole-genome shotgun hybrid approach (Sanger, 454 FLX). These genomes are smaller than those of phylogenetically related ascomycetes. The assembly of A. benhamiae spans 22.3 Mb and that of T. verrucosum comprises 22.6 Mb. The genomes of A. benhamiae and T. verrucosum are compact and only contain 7,980 and 8,024 predicted protein-encoding genes, respectively. Most of these genes lie in collinear regions and are shared between the two fungi suggesting a very recent speciation.

    As expected from their peculiar ecological niche, i.e. the animal skin, the two dermatophytes belong to the most protease-rich fungal species. They contain 235 protease-encoding genes, 87 of the predicted proteins having a secretion signal. A comprehensive analysis of the secretome during keratin degradation was carried out by combining 2D-PAGE and MALDI-TOF/TOF. RNA-Seq transcriptome profiling of A. benhamiae growing on human keratinocytes was performed to investigate the the entire process of infection. Subtilisin-like serine proteases, fungalysine-type metalloproteases, leucine aminopeptidases and dipeptidyl-peptidases are secreted during growth of A. benhamiae on keratin and keratinocytes. In addition, these dermatophytes can efficiently assimilate lipids, major constituents of the skin, thanks to the presence of 16 lipase genes. As discussed by the authors, the presence of large protease gene families in dermatophytes and their striking induction on keratin and human keratinocytes likely reflects selection during evolution and the ability of these fungi to adapt to different environmental conditions during infection and saprophytic growth. It appears that secondary metabolites also play a crucial role during keratinocyte infection.

    Burmester et al. (2011) Comparative and functional genomics provide insights into the pathogenicity of dermatophytic fungi. Genome Biology 12:R7

    Photo: A. benhamiae on human hair © Burmester et al.